Restaurants and cafeterias are constantly exposed to bacterial contamination. In such environments, it is highly needed the rapid bacteria detection system with simple pre-treatment device. To solve this problem, this study presented the pre-treatment device and Rapid electrochemical (REC) biosensor set for detecting Escherichia coli (E. coli) gene in milk sample. The pre-treatment device is consisted of tetraethyl orthosilicate (TEOS)-coated bead that operated with sonication method, and it can effectively remove the E. coli residues and extract E. coli DNA well. By analyzing the sequences of various foodborne pathogens, we selected the highly variable region sequences of E. coli DNA to use as the bioprobe for REC biosensor. The selected thiol-modified bioprobe was immobilized onto the fabricated biosensor electrode. For detecting the extracted E. coli gene fragment rapidly, the alternating current electrothermal flow (ACEF) technique was introduced to REC-biosensor. ACEF technique minimize the target-bioprobe binding time to 10 mins. Using the extracted E. coli DNA fragments with the pre-treatment device, the proposed REC-biosensor shows the limit of detection (LOD) in milk samples was 9.235 × 10-5 ng/μL, and the target detection accuracy was 92.5 %, with a maximal error rate up to 6.730 %. Moreover, the biosensor demonstrated high selectivity in electrochemical performance evaluation (Matrix effect = 7.425 %). The developed pre-treatment device provides simple and quick preprocessing time (within 20 min) of E. coli, and REC biosensor provides the rapid detection of E. coli (within 10 min). In conclusion, the proposed pre-treatment device and biosensor set can be easily applied to other types of bacteria, virus or germs in the near future.